Ratoon rice systems often require high nitrogen (N) inputs and environmental costs. Here, we conducted field trials to evaluate the synergistic effects of different N synergists coupled with 15% N reduction on the greenhouse gas emissions, yield, and net ecosystem economic benefits (NEEB) of ratoon rice systems in central China. Five treatments were designed and implemented, including farmers’ fertilization practice (FFP), 15% N reduction (FFP-15%), and the application of humic acid (HA), 3,4-dimethylpyrazole phosphate (DMPP), and DMPP+SiO₂ (DMPP+SI) based on FFP-15%. The results showed that compared with FFP, FFP-15% significantly decreased CH₄ emissions by 36.49% (p < 0.01) and global warming potential (GWP) by 35.33% (p < 0.01) but exhibited no enhancing effect on NEEB. Relative to FFP-15% treatment, HA treatment demonstrated more consistent multi-gas mitigation effects, which significantly reduced the annual NH₃ volatilization by 12.41% (from 40.58 kg N ha⁻¹ to 46.33 kg N ha⁻¹, p < 0.01), CH₄ emissions by 20.62% (p < 0.01), and N₂O emissions by 28.50% (p < 0.01), thereby lowering the GWP by 21.12% (from 7.32 t CO₂-eq. ha⁻¹ to 9.28 t CO₂-eq. ha⁻¹, p < 0.01). Nevertheless, this environmental efficacy was accompanied by a significant grain yield penalty of 5.77% (p < 0.01), probably due to the accumulation of more nutrients in stem sheaths (rather than in grains), which reduced grain nutrient allocation and ultimately resulted in no significant enhancement of NEEB. In contrast, DMPP-based treatments did not affect NH₃ volatilization and CH₄ emissions but markedly decreased N₂O emissions (by 19.00% for DMPP treatment, p < 0.01) and enhanced the grain yield (by 4.23% for DMPP treatment and 8.34% for DMPP+SI treatment, p < 0.01) relative to FFP-15% treatment. Although DMPP+SI treatment showed no significant effect on GWP or GHGI, it significantly enhanced the NEEB by 19.74% (p < 0.01) compared with FFP-15% treatment. In conclusion, integrating DMPP with SiO₂ application under N reduction represents a feasible management strategy to advance green, low-carbon production of ratoon rice systems in central China.